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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2022-04-01, 08:59 based on data in: /home/jhetzler/MiSeqOSL/seq/fastQC


        General Statistics

        Showing 400/400 rows and 3/5 columns.
        Sample Name% Dups% GCM Seqs
        A10_L001_R1_001
        92.4%
        41%
        0.0
        A10_L001_R2_001
        87.9%
        44%
        0.0
        A11_L001_R1_001
        92.8%
        43%
        0.0
        A11_L001_R2_001
        87.3%
        47%
        0.0
        A12_L001_R1_001
        97.3%
        49%
        0.0
        A12_L001_R2_001
        94.8%
        54%
        0.0
        A13_L001_R1_001
        85.7%
        36%
        0.0
        A13_L001_R2_001
        81.3%
        38%
        0.0
        A14_L001_R1_001
        87.2%
        36%
        0.0
        A14_L001_R2_001
        83.0%
        39%
        0.0
        A15_L001_R1_001
        89.4%
        37%
        0.0
        A15_L001_R2_001
        83.9%
        40%
        0.0
        A16_L001_R1_001
        90.9%
        38%
        0.0
        A16_L001_R2_001
        86.6%
        41%
        0.0
        A17_L001_R1_001
        88.8%
        38%
        0.0
        A17_L001_R2_001
        84.5%
        40%
        0.0
        A18_L001_R1_001
        89.0%
        37%
        0.0
        A18_L001_R2_001
        83.3%
        39%
        0.0
        A19_L001_R1_001
        85.0%
        37%
        0.0
        A19_L001_R2_001
        81.1%
        40%
        0.0
        A1_L001_R1_001
        93.4%
        44%
        0.0
        A1_L001_R2_001
        89.9%
        47%
        0.0
        A20_L001_R1_001
        90.4%
        37%
        0.0
        A20_L001_R2_001
        85.8%
        39%
        0.0
        A21_L001_R1_001
        88.2%
        38%
        0.0
        A21_L001_R2_001
        84.3%
        40%
        0.0
        A22_L001_R1_001
        88.9%
        38%
        0.0
        A22_L001_R2_001
        85.4%
        40%
        0.0
        A23_L001_R1_001
        89.4%
        37%
        0.0
        A23_L001_R2_001
        83.9%
        39%
        0.0
        A24_L001_R1_001
        86.6%
        38%
        0.0
        A24_L001_R2_001
        82.1%
        40%
        0.0
        A25_L001_R1_001
        90.1%
        36%
        0.0
        A25_L001_R2_001
        85.9%
        39%
        0.0
        A26_L001_R1_001
        88.6%
        37%
        0.0
        A26_L001_R2_001
        84.0%
        39%
        0.0
        A27_L001_R1_001
        89.0%
        37%
        0.0
        A27_L001_R2_001
        84.1%
        40%
        0.0
        A28_L001_R1_001
        93.1%
        47%
        0.0
        A28_L001_R2_001
        90.4%
        52%
        0.0
        A29_L001_R1_001
        89.2%
        37%
        0.0
        A29_L001_R2_001
        84.4%
        39%
        0.0
        A2_L001_R1_001
        81.2%
        30%
        0.0
        A2_L001_R2_001
        69.3%
        30%
        0.0
        A30_L001_R1_001
        89.1%
        38%
        0.0
        A30_L001_R2_001
        83.5%
        41%
        0.0
        A31_L001_R1_001
        88.8%
        38%
        0.0
        A31_L001_R2_001
        83.6%
        40%
        0.0
        A32_L001_R1_001
        87.6%
        38%
        0.0
        A32_L001_R2_001
        83.9%
        40%
        0.0
        A33_L001_R1_001
        82.4%
        38%
        0.0
        A33_L001_R2_001
        78.9%
        41%
        0.0
        A34_L001_R1_001
        83.0%
        38%
        0.0
        A34_L001_R2_001
        79.8%
        41%
        0.0
        A35_L001_R1_001
        88.8%
        38%
        0.0
        A35_L001_R2_001
        84.4%
        41%
        0.0
        A36_L001_R1_001
        85.0%
        37%
        0.0
        A36_L001_R2_001
        78.4%
        40%
        0.0
        A37_L001_R1_001
        89.9%
        37%
        0.0
        A37_L001_R2_001
        85.8%
        39%
        0.0
        A38_L001_R1_001
        89.4%
        37%
        0.0
        A38_L001_R2_001
        85.5%
        40%
        0.0
        A39_L001_R1_001
        84.2%
        38%
        0.0
        A39_L001_R2_001
        84.1%
        41%
        0.0
        A3_L001_R1_001
        91.6%
        42%
        0.0
        A3_L001_R2_001
        86.8%
        45%
        0.0
        A40_L001_R1_001
        84.7%
        37%
        0.0
        A40_L001_R2_001
        80.0%
        40%
        0.0
        A41_L001_R1_001
        89.2%
        37%
        0.0
        A41_L001_R2_001
        86.0%
        39%
        0.0
        A42_L001_R1_001
        88.0%
        37%
        0.0
        A42_L001_R2_001
        84.7%
        39%
        0.0
        A43_L001_R1_001
        84.5%
        37%
        0.0
        A43_L001_R2_001
        81.5%
        40%
        0.0
        A44_L001_R1_001
        88.5%
        36%
        0.0
        A44_L001_R2_001
        84.6%
        38%
        0.0
        A45_L001_R1_001
        89.5%
        40%
        0.0
        A45_L001_R2_001
        85.7%
        43%
        0.0
        A46_L001_R1_001
        90.1%
        37%
        0.0
        A46_L001_R2_001
        85.6%
        39%
        0.0
        A47_L001_R1_001
        88.9%
        37%
        0.0
        A47_L001_R2_001
        84.3%
        39%
        0.0
        A48_L001_R1_001
        88.0%
        37%
        0.0
        A48_L001_R2_001
        82.8%
        39%
        0.0
        A49_L001_R1_001
        82.8%
        37%
        0.0
        A49_L001_R2_001
        79.3%
        39%
        0.0
        A4_L001_R1_001
        91.8%
        40%
        0.0
        A4_L001_R2_001
        86.7%
        44%
        0.0
        A50_L001_R1_001
        87.2%
        37%
        0.0
        A50_L001_R2_001
        83.3%
        39%
        0.0
        A5_L001_R1_001
        93.6%
        43%
        0.0
        A5_L001_R2_001
        88.6%
        46%
        0.0
        A6_L001_R1_001
        92.9%
        41%
        0.0
        A6_L001_R2_001
        88.2%
        44%
        0.0
        A7_L001_R1_001
        92.9%
        43%
        0.0
        A7_L001_R2_001
        87.1%
        47%
        0.0
        A8_L001_R1_001
        87.7%
        45%
        0.0
        A8_L001_R2_001
        76.0%
        50%
        0.0
        A9_L001_R1_001
        92.6%
        42%
        0.0
        A9_L001_R2_001
        87.8%
        45%
        0.0
        B10_L001_R1_001
        91.4%
        43%
        0.0
        B10_L001_R2_001
        85.5%
        46%
        0.0
        B11_L001_R1_001
        91.3%
        41%
        0.0
        B11_L001_R2_001
        85.0%
        44%
        0.0
        B12_L001_R1_001
        82.9%
        30%
        0.0
        B12_L001_R2_001
        72.2%
        30%
        0.0
        B13_L001_R1_001
        86.6%
        37%
        0.0
        B13_L001_R2_001
        82.0%
        39%
        0.0
        B14_L001_R1_001
        86.3%
        36%
        0.0
        B14_L001_R2_001
        81.2%
        38%
        0.0
        B15_L001_R1_001
        82.1%
        36%
        0.0
        B15_L001_R2_001
        76.9%
        39%
        0.0
        B16_L001_R1_001
        87.9%
        35%
        0.0
        B16_L001_R2_001
        83.6%
        37%
        0.0
        B17_L001_R1_001
        87.7%
        36%
        0.0
        B17_L001_R2_001
        83.5%
        37%
        0.0
        B18_L001_R1_001
        87.8%
        36%
        0.0
        B18_L001_R2_001
        83.7%
        38%
        0.0
        B19_L001_R1_001
        87.8%
        36%
        0.0
        B19_L001_R2_001
        83.6%
        37%
        0.0
        B1_L001_R1_001
        90.2%
        39%
        0.0
        B1_L001_R2_001
        86.3%
        42%
        0.0
        B20_L001_R1_001
        86.9%
        35%
        0.0
        B20_L001_R2_001
        82.2%
        37%
        0.0
        B21_L001_R1_001
        85.9%
        33%
        0.0
        B21_L001_R2_001
        81.4%
        34%
        0.0
        B22_L001_R1_001
        86.8%
        33%
        0.0
        B22_L001_R2_001
        81.8%
        34%
        0.0
        B23_L001_R1_001
        88.2%
        35%
        0.0
        B23_L001_R2_001
        84.5%
        37%
        0.0
        B24_L001_R1_001
        89.9%
        35%
        0.0
        B24_L001_R2_001
        85.3%
        37%
        0.0
        B25_L001_R1_001
        87.7%
        36%
        0.0
        B25_L001_R2_001
        83.1%
        37%
        0.0
        B26_L001_R1_001
        88.8%
        36%
        0.0
        B26_L001_R2_001
        84.3%
        38%
        0.0
        B27_L001_R1_001
        88.5%
        36%
        0.0
        B27_L001_R2_001
        84.4%
        37%
        0.0
        B28_L001_R1_001
        89.3%
        35%
        0.0
        B28_L001_R2_001
        84.6%
        36%
        0.0
        B29_L001_R1_001
        77.4%
        34%
        0.1
        B29_L001_R2_001
        70.7%
        37%
        0.1
        B2_L001_R1_001
        90.3%
        39%
        0.0
        B2_L001_R2_001
        85.0%
        42%
        0.0
        B30_L001_R1_001
        88.3%
        34%
        0.0
        B30_L001_R2_001
        82.6%
        36%
        0.0
        B31_L001_R1_001
        88.5%
        36%
        0.0
        B31_L001_R2_001
        84.6%
        37%
        0.0
        B32_L001_R1_001
        88.2%
        37%
        0.0
        B32_L001_R2_001
        84.2%
        39%
        0.0
        B33_L001_R1_001
        88.1%
        37%
        0.0
        B33_L001_R2_001
        84.3%
        39%
        0.0
        B34_L001_R1_001
        84.8%
        37%
        0.0
        B34_L001_R2_001
        78.9%
        40%
        0.0
        B35_L001_R1_001
        89.2%
        35%
        0.0
        B35_L001_R2_001
        84.7%
        37%
        0.0
        B36_L001_R1_001
        87.0%
        36%
        0.0
        B36_L001_R2_001
        81.9%
        38%
        0.0
        B37_L001_R1_001
        86.0%
        36%
        0.0
        B37_L001_R2_001
        80.1%
        39%
        0.0
        B38_L001_R1_001
        88.0%
        38%
        0.0
        B38_L001_R2_001
        82.5%
        40%
        0.0
        B39_L001_R1_001
        86.6%
        38%
        0.0
        B39_L001_R2_001
        82.6%
        40%
        0.0
        B3_L001_R1_001
        90.6%
        45%
        0.0
        B3_L001_R2_001
        83.6%
        49%
        0.0
        B40_L001_R1_001
        90.3%
        39%
        0.0
        B40_L001_R2_001
        86.4%
        41%
        0.0
        B41_L001_R1_001
        82.9%
        41%
        0.0
        B41_L001_R2_001
        78.2%
        44%
        0.0
        B42_L001_R1_001
        86.4%
        38%
        0.0
        B42_L001_R2_001
        81.7%
        40%
        0.0
        B43_L001_R1_001
        87.5%
        37%
        0.0
        B43_L001_R2_001
        80.3%
        39%
        0.0
        B44_L001_R1_001
        87.9%
        37%
        0.0
        B44_L001_R2_001
        82.7%
        40%
        0.0
        B45_L001_R1_001
        86.7%
        36%
        0.0
        B45_L001_R2_001
        82.3%
        39%
        0.0
        B46_L001_R1_001
        84.7%
        36%
        0.0
        B46_L001_R2_001
        80.1%
        39%
        0.0
        B47_L001_R1_001
        85.4%
        37%
        0.0
        B47_L001_R2_001
        80.5%
        40%
        0.0
        B48_L001_R1_001
        86.6%
        38%
        0.0
        B48_L001_R2_001
        79.7%
        40%
        0.0
        B49_L001_R1_001
        88.0%
        38%
        0.0
        B49_L001_R2_001
        81.5%
        40%
        0.0
        B4_L001_R1_001
        91.2%
        40%
        0.0
        B4_L001_R2_001
        86.4%
        42%
        0.0
        B50_L001_R1_001
        85.3%
        36%
        0.0
        B50_L001_R2_001
        78.2%
        37%
        0.0
        B5_L001_R1_001
        89.8%
        42%
        0.0
        B5_L001_R2_001
        83.8%
        45%
        0.0
        B6_L001_R1_001
        91.5%
        41%
        0.0
        B6_L001_R2_001
        86.1%
        45%
        0.0
        B7_L001_R1_001
        92.7%
        47%
        0.0
        B7_L001_R2_001
        88.3%
        52%
        0.0
        B8_L001_R1_001
        89.7%
        41%
        0.0
        B8_L001_R2_001
        83.2%
        44%
        0.0
        B9_L001_R1_001
        90.6%
        39%
        0.0
        B9_L001_R2_001
        85.0%
        42%
        0.0
        C10_L001_R1_001
        91.2%
        37%
        0.0
        C10_L001_R2_001
        87.0%
        39%
        0.0
        C11_L001_R1_001
        91.0%
        37%
        0.0
        C11_L001_R2_001
        86.6%
        40%
        0.0
        C12_L001_R1_001
        90.7%
        36%
        0.0
        C12_L001_R2_001
        86.7%
        38%
        0.0
        C13_L001_R1_001
        90.8%
        37%
        0.0
        C13_L001_R2_001
        86.9%
        39%
        0.0
        C14_L001_R1_001
        90.4%
        37%
        0.0
        C14_L001_R2_001
        85.8%
        39%
        0.0
        C15_L001_R1_001
        91.3%
        37%
        0.0
        C15_L001_R2_001
        87.3%
        39%
        0.0
        C16_L001_R1_001
        90.5%
        36%
        0.0
        C16_L001_R2_001
        86.3%
        37%
        0.0
        C17_L001_R1_001
        88.1%
        35%
        0.0
        C17_L001_R2_001
        83.3%
        37%
        0.0
        C18_L001_R1_001
        83.5%
        38%
        0.0
        C18_L001_R2_001
        77.3%
        41%
        0.0
        C19_L001_R1_001
        89.8%
        37%
        0.0
        C19_L001_R2_001
        84.9%
        39%
        0.0
        C1_L001_R1_001
        89.0%
        38%
        0.0
        C1_L001_R2_001
        83.7%
        41%
        0.0
        C20_L001_R1_001
        89.8%
        36%
        0.0
        C20_L001_R2_001
        84.8%
        39%
        0.0
        C21_L001_R1_001
        87.6%
        38%
        0.0
        C21_L001_R2_001
        81.5%
        41%
        0.0
        C22_L001_R1_001
        88.6%
        37%
        0.0
        C22_L001_R2_001
        83.5%
        40%
        0.0
        C23_L001_R1_001
        91.4%
        38%
        0.0
        C23_L001_R2_001
        86.8%
        40%
        0.0
        C24_L001_R1_001
        90.8%
        37%
        0.0
        C24_L001_R2_001
        85.9%
        40%
        0.0
        C25_L001_R1_001
        82.5%
        39%
        0.0
        C25_L001_R2_001
        79.1%
        42%
        0.0
        C26_L001_R1_001
        88.9%
        37%
        0.0
        C26_L001_R2_001
        83.7%
        40%
        0.0
        C27_L001_R1_001
        87.9%
        37%
        0.0
        C27_L001_R2_001
        81.8%
        40%
        0.0
        C28_L001_R1_001
        90.1%
        38%
        0.0
        C28_L001_R2_001
        85.4%
        40%
        0.0
        C29_L001_R1_001
        87.7%
        38%
        0.0
        C29_L001_R2_001
        83.7%
        40%
        0.0
        C2_L001_R1_001
        88.9%
        40%
        0.0
        C2_L001_R2_001
        83.5%
        42%
        0.0
        C30_L001_R1_001
        86.9%
        38%
        0.0
        C30_L001_R2_001
        83.4%
        40%
        0.0
        C31_L001_R1_001
        92.5%
        44%
        0.0
        C31_L001_R2_001
        89.5%
        46%
        0.0
        C32_L001_R1_001
        89.8%
        39%
        0.0
        C32_L001_R2_001
        84.4%
        41%
        0.0
        C33_L001_R1_001
        89.6%
        39%
        0.0
        C33_L001_R2_001
        84.6%
        41%
        0.0
        C34_L001_R1_001
        84.8%
        40%
        0.0
        C34_L001_R2_001
        80.0%
        43%
        0.0
        C35_L001_R1_001
        88.8%
        41%
        0.0
        C35_L001_R2_001
        83.0%
        44%
        0.0
        C36_L001_R1_001
        88.8%
        37%
        0.0
        C36_L001_R2_001
        84.5%
        40%
        0.0
        C37_L001_R1_001
        89.2%
        38%
        0.0
        C37_L001_R2_001
        85.1%
        40%
        0.0
        C38_L001_R1_001
        88.0%
        38%
        0.0
        C38_L001_R2_001
        83.9%
        40%
        0.0
        C39_L001_R1_001
        89.0%
        38%
        0.0
        C39_L001_R2_001
        85.1%
        41%
        0.0
        C3_L001_R1_001
        88.0%
        40%
        0.0
        C3_L001_R2_001
        81.5%
        43%
        0.0
        C40_L001_R1_001
        89.2%
        40%
        0.0
        C40_L001_R2_001
        84.2%
        44%
        0.0
        C41_L001_R1_001
        85.3%
        30%
        0.0
        C41_L001_R2_001
        80.2%
        30%
        0.0
        C42_L001_R1_001
        84.3%
        31%
        0.0
        C42_L001_R2_001
        76.9%
        31%
        0.0
        C43_L001_R1_001
        83.3%
        31%
        0.0
        C43_L001_R2_001
        77.2%
        32%
        0.0
        C44_L001_R1_001
        82.2%
        31%
        0.0
        C44_L001_R2_001
        76.4%
        31%
        0.0
        C45_L001_R1_001
        78.7%
        31%
        0.0
        C45_L001_R2_001
        73.6%
        32%
        0.0
        C46_L001_R1_001
        82.0%
        31%
        0.0
        C46_L001_R2_001
        76.4%
        31%
        0.0
        C47_L001_R1_001
        86.5%
        30%
        0.0
        C47_L001_R2_001
        80.3%
        31%
        0.0
        C48_L001_R1_001
        82.6%
        30%
        0.0
        C48_L001_R2_001
        77.7%
        31%
        0.0
        C49_L001_R1_001
        88.7%
        38%
        0.0
        C49_L001_R2_001
        83.8%
        40%
        0.0
        C4_L001_R1_001
        88.5%
        36%
        0.0
        C4_L001_R2_001
        84.2%
        38%
        0.0
        C50_L001_R1_001
        87.2%
        38%
        0.0
        C50_L001_R2_001
        82.6%
        40%
        0.0
        C5_L001_R1_001
        89.4%
        36%
        0.0
        C5_L001_R2_001
        84.4%
        38%
        0.0
        C6_L001_R1_001
        87.6%
        37%
        0.0
        C6_L001_R2_001
        82.9%
        39%
        0.0
        C7_L001_R1_001
        89.9%
        37%
        0.0
        C7_L001_R2_001
        85.1%
        39%
        0.0
        C8_L001_R1_001
        91.0%
        37%
        0.0
        C8_L001_R2_001
        86.7%
        39%
        0.0
        C9_L001_R1_001
        91.1%
        36%
        0.0
        C9_L001_R2_001
        87.1%
        38%
        0.0
        D10_L001_R1_001
        89.0%
        36%
        0.0
        D10_L001_R2_001
        84.4%
        38%
        0.0
        D11_L001_R1_001
        87.6%
        36%
        0.0
        D11_L001_R2_001
        83.2%
        38%
        0.0
        D12_L001_R1_001
        86.5%
        36%
        0.0
        D12_L001_R2_001
        82.9%
        39%
        0.0
        D13_L001_R1_001
        89.1%
        37%
        0.0
        D13_L001_R2_001
        84.6%
        38%
        0.0
        D14_L001_R1_001
        87.6%
        37%
        0.0
        D14_L001_R2_001
        82.3%
        39%
        0.0
        D15_L001_R1_001
        83.4%
        37%
        0.0
        D15_L001_R2_001
        77.9%
        40%
        0.0
        D16_L001_R1_001
        90.9%
        36%
        0.0
        D16_L001_R2_001
        85.7%
        38%
        0.0
        D17_L001_R1_001
        87.8%
        37%
        0.0
        D17_L001_R2_001
        82.4%
        40%
        0.0
        D18_L001_R1_001
        89.1%
        37%
        0.0
        D18_L001_R2_001
        84.1%
        39%
        0.0
        D19_L001_R1_001
        75.1%
        37%
        0.0
        D19_L001_R2_001
        71.9%
        40%
        0.0
        D1_L001_R1_001
        90.3%
        39%
        0.0
        D1_L001_R2_001
        86.9%
        41%
        0.0
        D20_L001_R1_001
        89.1%
        37%
        0.0
        D20_L001_R2_001
        84.8%
        38%
        0.0
        D21_L001_R1_001
        84.7%
        37%
        0.0
        D21_L001_R2_001
        81.2%
        40%
        0.0
        D22_L001_R1_001
        79.8%
        38%
        0.0
        D22_L001_R2_001
        76.6%
        41%
        0.0
        D23_L001_R1_001
        89.5%
        36%
        0.0
        D23_L001_R2_001
        85.3%
        38%
        0.0
        D24_L001_R1_001
        77.8%
        39%
        0.0
        D24_L001_R2_001
        79.6%
        43%
        0.0
        D25_L001_R1_001
        85.0%
        34%
        0.0
        D25_L001_R2_001
        83.1%
        36%
        0.0
        D26_L001_R1_001
        87.8%
        35%
        0.0
        D26_L001_R2_001
        83.0%
        37%
        0.0
        D27_L001_R1_001
        84.9%
        36%
        0.0
        D27_L001_R2_001
        80.7%
        38%
        0.0
        D28_L001_R1_001
        85.5%
        36%
        0.0
        D28_L001_R2_001
        81.6%
        38%
        0.0
        D29_L001_R1_001
        72.1%
        40%
        0.0
        D29_L001_R2_001
        74.3%
        44%
        0.0
        D2_L001_R1_001
        83.6%
        37%
        0.0
        D2_L001_R2_001
        80.1%
        40%
        0.0
        D30_L001_R1_001
        88.3%
        36%
        0.0
        D30_L001_R2_001
        83.2%
        38%
        0.0
        D31_L001_R1_001
        87.1%
        37%
        0.0
        D31_L001_R2_001
        83.0%
        39%
        0.0
        D32_L001_R1_001
        83.2%
        37%
        0.0
        D32_L001_R2_001
        79.7%
        39%
        0.0
        D33_L001_R1_001
        83.7%
        36%
        0.0
        D33_L001_R2_001
        79.4%
        38%
        0.0
        D34_L001_R1_001
        87.0%
        36%
        0.0
        D34_L001_R2_001
        82.4%
        39%
        0.0
        D35_L001_R1_001
        86.8%
        36%
        0.0
        D35_L001_R2_001
        82.6%
        38%
        0.0
        D36_L001_R1_001
        87.6%
        36%
        0.0
        D36_L001_R2_001
        81.6%
        38%
        0.0
        D37_L001_R1_001
        86.1%
        36%
        0.0
        D37_L001_R2_001
        81.2%
        39%
        0.0
        D38_L001_R1_001
        77.6%
        37%
        0.0
        D38_L001_R2_001
        72.8%
        40%
        0.0
        D39_L001_R1_001
        88.3%
        37%
        0.0
        D39_L001_R2_001
        85.5%
        39%
        0.0
        D3_L001_R1_001
        82.2%
        38%
        0.0
        D3_L001_R2_001
        80.7%
        41%
        0.0
        D40_L001_R1_001
        88.3%
        37%
        0.0
        D40_L001_R2_001
        83.0%
        40%
        0.0
        D41_L001_R1_001
        87.2%
        38%
        0.0
        D41_L001_R2_001
        83.5%
        40%
        0.0
        D42_L001_R1_001
        74.2%
        37%
        0.0
        D42_L001_R2_001
        70.7%
        40%
        0.0
        D43_L001_R1_001
        87.6%
        37%
        0.0
        D43_L001_R2_001
        84.9%
        40%
        0.0
        D44_L001_R1_001
        78.8%
        39%
        0.0
        D44_L001_R2_001
        63.0%
        43%
        0.0
        D45_L001_R1_001
        78.3%
        38%
        0.0
        D45_L001_R2_001
        73.4%
        40%
        0.0
        D46_L001_R1_001
        78.6%
        37%
        0.0
        D46_L001_R2_001
        79.7%
        40%
        0.0
        D47_L001_R1_001
        83.8%
        36%
        0.0
        D47_L001_R2_001
        79.5%
        38%
        0.0
        D48_L001_R1_001
        89.5%
        36%
        0.0
        D48_L001_R2_001
        82.9%
        38%
        0.0
        D49_L001_R1_001
        87.1%
        38%
        0.0
        D49_L001_R2_001
        81.5%
        40%
        0.0
        D4_L001_R1_001
        89.3%
        36%
        0.0
        D4_L001_R2_001
        84.6%
        38%
        0.0
        D50_L001_R1_001
        86.3%
        37%
        0.0
        D50_L001_R2_001
        80.9%
        39%
        0.0
        D5_L001_R1_001
        89.4%
        36%
        0.0
        D5_L001_R2_001
        84.7%
        38%
        0.0
        D6_L001_R1_001
        89.0%
        36%
        0.0
        D6_L001_R2_001
        84.4%
        38%
        0.0
        D7_L001_R1_001
        88.8%
        36%
        0.0
        D7_L001_R2_001
        84.5%
        38%
        0.0
        D8_L001_R1_001
        90.4%
        38%
        0.0
        D8_L001_R2_001
        85.8%
        40%
        0.0
        D9_L001_R1_001
        83.3%
        37%
        0.0
        D9_L001_R2_001
        78.3%
        39%
        0.0

        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution

        All samples have sequences of a single length (301bp).

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

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